Annotated gene sequence

Experiment = in vivo icSHAPE / NAI-N3 RefSeq = hg38 Cell = HEK293T Original Data Reference = Cell. 2016;165(5):1267-1279.

stable secondary structure loop bulge/internal loop no SHAPE data coding sequence

GCTTTCGCGAGGTTTTGACTCTCGTGGCGCCCCAGGGGCCGACGGGAGTGGCGGCCGCGCGGAGGAGGCCAAGATGGCGGCAGCTGCGGCTTCGCTTCGC
GGGGTAGTGTTGGGCCCGCGGGGCGCGGGGCTCCCGGGCGCGCGTGCCCGGGGTCTGCTGTGCAGCGCGCGTCCCGGGCAGCTCCCGCTACGGACACCTC
AGGCAGTGGCCTTGTCGTCGAAGTCTGGCCTTTCCCGAGGCCGGAAAGTGATGCTGTCAGCGCTGGGCATGCTGGCGGCAGGGGGTGCGGGGCTGGCCAT
GGCTCTGCATTCGGCTGTGAGTGCCAGTGACCTGGAGCTGCACCCCCCCAGCTATCCGTGGTCTCACCGTGGCCTCCTCTCTTCCTTGGACCACACCAGC
ATCCGGAGGGGTTTCCAGGTATATAAGCAGGTGTGCGCCTCCTGCCACAGCATGGACTTCGTGGCCTACCGCCACCTGGTGGGCGTGTGCTACACGGAGG
ATGAAGCTAAGGAGCTGGCTGCGGAGGTGGAGGTTCAAGACGGCCCCAATGAAGATGGGGAGATGTTCATGCGGCCAGGGAAGCTGTTCGACTATTTCCC
AAAACCATACCCCAACAGTGAGGCTGCTCGAGCTGCCAACAACGGAGCATTGCCCCCTGACCTCAGCTACATCGTGCGAGCTAGGCATGGTGGTGAGGAC
TACGTCTTCTCCCTGCTCACGGGCTACTGCGAGCCACCCACCGGGGTGTCACTGCGGGAAGGTCTCTACTTCAACCCCTACTTTCCTGGCCAGGCCATTG
CCATGGCCCCTCCCATCTACACAGATGTCTTAGAGTTTGACGATGGCACCCCAGCTACCATGTCCCAGATAGCCAAGGATGTGTGCACCTTCCTGCGCTG
GGCATCTGAGCCAGAGCACGACCATCGAAAACGCATGGGGCTCAAGATGTTGATGATGATGGCTCTGCTGGTGCCCCTGGTCTACACCATAAAGCGGCAC
AAGTGGTCAGTCCTGAAGAGTCGGAAGCTGGCATATCGGCCGCCCAAGTGACCCTGTCCAGTGTCTGCTTGCCATCCTGCCAGAACAGGCCCTCAAGCCC
AAGAGCCATCCCAGGCCTGTTCAGGCCTCAGCTAAGCCTCTCTTCATCTGGAAGAAGAGGCAAGGGGGCAGGAGACCAGGCTCTAGCTCTGGGCCCTCCT
TCAGCCCCCATCATGGGAATAAATTAATTTTCTCAATGTA

Loop counts:

3 nts: 2
4 nts: 11
5 nts: 1
6 nts: 1

Tetra-loop variants:

GUCC    1
AGUG    1
UCCC    1
GGGU    1
AAGG    1
GCUA    1
CAUU    1
ACAC    1
AAAA    1
CUAC    1
AGAG    1

Single bulge variants:

G x 0 bulge: 0
A x 0 bulge: 1
U x 0 bulge: 1
C x 0 bulge: 1

1 x 1 internal loop variants:

G x G bulge: 0
G x A bulge: 0
G x U bulge: 0
G x C bulge: 0
A x G bulge: 0
A x A bulge: 0
A x U bulge: 0
A x C bulge: 2
U x G bulge: 0
U x A bulge: 0
U x U bulge: 0
U x C bulge: 1
C x G bulge: 0
C x A bulge: 2
C x U bulge: 1
C x C bulge: 0